Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid

Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes

“…Gene modelling was performed using BRAKER2 27 – 39 on the softmasked E. scolopes reference genome 8 . The PacBio Iso-Seq data for E. scolopes newly generated here, published Illumina RNA-seq data (mapped as in 16 ) for E. scolopes , and publicly available protein hints files from Doryteuthis pealeii 10 , Octopus bimaculoides 10 , Nautilus pompilius 40 , Pecten maximus 41 and Branchiostoma floridae 42 were used for training (Table 1 ). Both Illumina RNA-seq and PacBio Iso-Seq were inputted into BRAKER2 using the —bam option, whilst protein files were specified with the–prot_seq option.…”

“…More recently, E. scolopes has also become a central model for genome evolution research 8 – 10 , 16 These studies have identified genome-wide rearrangement events 10 and putatively novel regulatory landscape associated with them 8 . These recent genomic insights pave the way for further understanding of coleoid cephalopod gene regulation and genomic evolutionary trends that have been hypothesised to be associated with some key coleoid innovations.…”

“…This manuscript describes an ongoing effort to alleviate this bottleneck by creating and refining gene annotation in the E. scolopes genome using a plethora of publicly available transcriptomic and protein sequence data 12 , 16 with newly generated long-read transcriptomic sequencing (Table 1 ). PacBio Iso-Seq sequencing yielded 195,212 reads, with at least 98% of reads mapped to the genome per sample.…”

“…Note all PacBio Iso-Seq and Illumina RNA-seq samples used were from male individuals except the ovary sample. Illumina short read RNA-seq samples were published (and mapped as in 16 ) and protein hints files were publicly available from 10 , 40 – 42 .…”